+Open data
-Basic information
Entry | Database: PDB / ID: 5gnc | ||||||
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Title | Crystal structure of Phytophthora. sojae PSR2 | ||||||
Components | Avh146 | ||||||
Keywords | UNKNOWN FUNCTION / PSR2 / RNAi | ||||||
Function / homology | host cell / extracellular region / RxLR effector protein PSR2 Function and homology information | ||||||
Biological species | Phytophthora sojae (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | He, J.Q. / Wu, B.X. / Ma, J.B. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Structural analysis ofPhytophthorasuppressor of RNA silencing 2 (PSR2) reveals a conserved modular fold contributing to virulence. Authors: He, J.Q. / Ye, W.W. / Choi, D.S. / Wu, B.X. / Zhai, Y. / Guo, B.D. / Duan, S.Y. / Wang, Y.C. / Gan, J.H. / Ma, W.B. / Ma, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gnc.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gnc.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/5gnc ftp://data.pdbj.org/pub/pdb/validation_reports/gn/5gnc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 68991.922 Da / Num. of mol.: 1 / Fragment: UNP residues 59-670 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora sojae (eukaryote) / Gene: Avh / Production host: Escherichia coli (E. coli) / References: UniProt: E0W4V5 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M NH4COOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 18820 / % possible obs: 98.76 % / Redundancy: 7.2 % / Net I/σ(I): 2.8 |
-Processing
Software |
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Refinement | Resolution: 2.8→30 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→51.144 Å
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Refine LS restraints |
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LS refinement shell |
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